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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgctccactgtctaagtttcccaacctccatcctactgattaatattgcaaatcttttcttaatacccaaaattttgcaaatactttctttaataccctaaatttgctgccagGCACTTGCTATTCTCATGGAGTACATTAACAAGGATGACACAAACATTCGGATTGGGGCAATCTTGGGTCTTGGTATTGCATATGCGGGTTCTCAGAAAG

Basic information

species Oryza sativa
transcript LOC_Os02g05340.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM2G155384_T03 (Zea mays), 3'ss of exon 15
gtatgtgctccactgtctaagtttcccaacctccatcctactgattaatattgcaaatcttttcttaatacccaaaattttgcaaatactttctttaataccctaaatttgctgccagGCACTTGCTATTCTCATGGAGTACATTAACAAGGATGACACAAACATTCGGATTGGGGCAATCTTGGGTCTTGGTATTGCATATGCGGGTTCTCAGAAAG
||| ||| |||||| | | || | | |  || || |||  |          ||||  |||| | ||                        | |  |||||||||||  || |||||||||  |||||||||| |||||||| |||  |||||||||| |||||||||| ||||| ||||| ||||||||||| ||||||||||| ||||| |||||||
gtaagtggtccactttgttagctactctccccccgtcccccc---------tgca--tcttctttt------------------------tcccctaataccctaacctttctgccagGCGTTTGCTATTCTTATGGAGTATATTGGCAAGGATGACTCAAACATTCGTATTGGAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAG

upper sequence: LOC_Os02g05340.1 (Oryza sativa), 3'ss of exon 15
lower sequence: GRMZM5G816609_T01 (Zea mays), 3'ss of exon 1
gtatgtgctccactgtctaagtttcccaacctccatcctac-tgattaatattgcaaatcttttcttaatacccaaaattttgcaaatacttt-ctttaataccctaaatttgctgccagGCACTTGCTATTCTCATGGAGTACATTAACAAGGATGACACAAACATTCGGATTGGGGCAATCTTGGGTCTTGGTATTGCATATGCGGGTTCTCAGAAAG
                                      ||  || |  |  |||  |  ||| |||| |  ||    |   ||||  |  ||| |  ||||||||| | ||| || ||||||  ||||||||||||||||||| |||  ||| |||||| |||||||||| ||||| ||||| ||||||||||| ||||||||||| ||||| |||||||
-------------------------------------gtatgtgctccactttgttag-cttgtcttgaccccttgcaccctgcatctttttttccctaataccctcacttttctaccagGCGTTTGCTATTCTCATGGAGTATATTGGCAAAGATGACTCAAACATTCGTATTGGAGCAATATTGGGTCTTGGAATTGCATATGCTGGTTCCCAGAAAG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|58686460|gb|CK075147.1|CK075147
EST:     TGCTAGGTATTGGTATTGTCACATGTGGTGTGAAGAATGATTGTGATCCA                         GCACTTGCTATTCTCATGGAGTACATTAACAAGGATGACACAAACATTCGG
genomic: TGCTAGGTATTGGTATTGTCACATGTGGTGTGAAGAATGATTGTGATCCAgtatgtgctc ... ttgctgccagGCACTTGCTATTCTCATGGAGTACATTAACAAGGATGACACAAACATTCGG
EST: gi|58589708|gb|CF988016.1|CF988016
EST:     TGCTAGGTATTGGTATTGTCACATGTGGTGTGAAGAATGATTGTGATCCA                         GCACGGGCTATTCTCATGGAGTACATTAACAAGGATGACACAAACATTCGG
genomic: TGCTAGGTATTGGTATTGTCACATGTGGTGTGAAGAATGATTGTGATCCAgtatgtgctc ... ttgctgccagGCACTTGCTATTCTCATGGAGTACATTAACAAGGATGACACAAACATTCGG
EST: gi|29667414|gb|CB663689.1|CB663689
EST:     TGCTAGGTATTGGTATTGTCACATGTGGTGTGAAGAATGATTGTGATCCA                         GCACTTGCTATTCTCATGGAGTACATTAACTAGGATGACA
genomic: TGCTAGGTATTGGTATTGTCACATGTGGTGTGAAGAATGATTGTGATCCAgtatgtgctc ... ttgctgccagGCACTTGCTATTCTCATGGAGTACATTAACAAGGATGACA
EST: gi|29671491|gb|CB667766.1|CB667766
EST:     TGCTAGGTATTGGTATTGTCACATGTGGTGTGAAGAATGATTGTGATCCA                         GCACTTGCTATTCTCATGGAGTACATTAACAAGGATGACACAAACATTCGG
genomic: TGCTAGGTATTGGTATTGTCACATGTGGTGTGAAGAATGATTGTGATCCAgtatgtgctc ... ttgctgccagGCACTTGCTATTCTCATGGAGTACATTAACAAGGATGACACAAACATTCGG
EST: gi|58604809|gb|CK015337.1|CK015337
EST:     TGCTAGGTATTGGTATTGTCACATGTGGTGTGAAGAATGATTGTGATCCA                         GCACTTGCTATTCTCATGGAGTACATTAACAAGGATGACACAAACATTCGG
genomic: TGCTAGGTATTGGTATTGTCACATGTGGTGTGAAGAATGATTGTGATCCAgtatgtgctc ... ttgctgccagGCACTTGCTATTCTCATGGAGTACATTAACAAGGATGACACAAACATTCGG
EST: gi|58685643|gb|CK074330.1|CK074330
EST:     TGCTAGGTATTGGTATTGTCACATGTGGTGTGAAGAATGATTGTGATCCA                         GCACTTGCTATTCTCATGGAGTACATTAACAAGGATGACACAAACATTCGG
genomic: TGCTAGGTATTGGTATTGTCACATGTGGTGTGAAGAATGATTGTGATCCAgtatgtgctc ... ttgctgccagGCACTTGCTATTCTCATGGAGTACATTAACAAGGATGACACAAACATTCGG
EST: gi|58605592|gb|CK033625.1|CK033625
EST:     TGCTAGGTATTGGTATTGTCACATGTGGTGTGAAGAATGATTGTGATCCA                         GCACTTGCTATTCTCATGGAGTACATTAACAAGGATGACACAAACATTCGG
genomic: TGCTAGGTATTGGTATTGTCACATGTGGTGTGAAGAATGATTGTGATCCAgtatgtgctc ... ttgctgccagGCACTTGCTATTCTCATGGAGTACATTAACAAGGATGACACAAACATTCGG
EST: gi|29634005|gb|CB639014.1|CB639014
EST:     TGCTAGGTATTGGTATTGTCACATGTGGTGTGAAGAATGATTGTGATCCA                         GCACTTGCTATTCTCATGGAGTACATTAACAAGGATGACACAAACATTCGG
genomic: TGCTAGGTATTGGTATTGTCACATGTGGTGTGAAGAATGATTGTGATCCAgtatgtgctc ... ttgctgccagGCACTTGCTATTCTCATGGAGTACATTAACAAGGATGACACAAACATTCGG
EST: gi|58681049|gb|CK069736.1|CK069736
EST:     TGCTAGGTATTGGTATTGTCACATGTGGTGTGAAGAATGATTGTGATCCA                         GCACTTGCTATTCTCATGGAGTACATTAACAAGGATGACACAAACATTCGG
genomic: TGCTAGGTATTGGTATTGTCACATGTGGTGTGAAGAATGATTGTGATCCAgtatgtgctc ... ttgctgccagGCACTTGCTATTCTCATGGAGTACATTAACAAGGATGACACAAACATTCGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 74 (downstream exon)
Score: 51

GCTTGACAAGTACTTACATAGTAATGATGCTCATGTTGTTGCTGGAGCTTTGCTAGGTATTGGTATTGTCACATGTGGTGTGAAGAATGATTGTGATCCAgtatgtgctc ... ttgctgccagGCACTTGCTATTCTCATGGAGTACATTAACAAGGATGACACAAACATTCGGATTGGGGCAATCTTGGGTCTTGGTATTGCATATGCGGGTTCTCAGAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaatacccaaaattttgcaaatactttctttaataccctaaatttgctgccagGCACTTGCTATTCTCATGGAGTACATTAACAAGGATGACACAAACATTCGGATTGGGGCAATCTTGGGTCTTGGTATTGCATATGCGGGTTCTCAGAAAG
                                     ccctaaa  putative branch site (score: 51)
          aaaattttgcaaatac  TA-rich tract